Nextflow workflow report

[curious_meitner]

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (SAMPLE_PAIRED_END_1_1)'

Caused by:
  Process `NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (SAMPLE_PAIRED_END_1_1)` terminated with an error exit status (1)


Command executed:

  INDEX=`find -L ./ -name "*.amb" | sed 's/\.amb$//'`
  
  bwa-mem2 \
      mem \
       \
      -t 2 \
      $INDEX \
      Bpacificus-ATCC10987-rep1-sWGS-MiSeqi100-241111_S1_L001_R1_001.fastq.gz Bpacificus-ATCC10987-rep1-sWGS-MiSeqi100-241111_S1_L001_R2_001.fastq.gz \
      | samtools sort  -@ 2  -o SAMPLE_PAIRED_END_1_1.bam -
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM":
      bwamem2: $(echo $(bwa-mem2 version 2>&1) | sed 's/.* //')
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
  Looking to launch executable "/opt/conda/bin/bwa-mem2.sse42", simd = .sse42
  Launching executable "/opt/conda/bin/bwa-mem2.sse42"
  -----------------------------
  Executing in SSE4.2 mode!!
  -----------------------------
  * SA compression enabled with xfactor: 8
  * Ref file: ./genome.fa
  * Entering FMI_search
  ERROR! Unable to open the file: ./genome.fa.bwt.2bit.64
  [W::hts_set_opt] Cannot change block size for this format
  samtools sort: failed to read header from "-"

Work dir:
  /Users/agrimabhatt/seqinspector/work/d0/4c595c9b0edfe8a64a1469cacb13c0

Container:
  community.wave.seqera.io/library/bwa-mem2_htslib_samtools:e1f420694f8e42bd

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Run times
14-Oct-2025 14:37:37 - 14-Oct-2025 14:38:17 (duration: 40.3s)
  4 succeeded  
  0 cached  
  0 ignored  
  2 failed (0 retries)  
Nextflow command
nextflow run main.nf -profile test,docker --input /Users/agrimabhatt/pipeline/testdata/testdata/Miseq_PairedEnd/samplesheet.csv --outdir result_test --bwa_index /Users/agrimabhatt/seqinspector/result/bwamem2_index/bwamem2/ -with-report
CPU-Hours
(a few seconds)
Launch directory
/Users/agrimabhatt/seqinspector
Work directory
/Users/agrimabhatt/seqinspector/work
Project directory
/Users/agrimabhatt/seqinspector
Script name
main.nf
Script ID
51ae67c7a1786a7937e7c520871990bd
Workflow session
b0c36634-5b3a-4877-8ce8-9ddc72aa08b5
Workflow profile
test,docker
Nextflow version
version 25.04.7, build 5955 (08-09-2025 13:29 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.

(tasks table omitted because the dataset is too big)